Research workbench
The glycogen-binding domain of the AMP-activated protein kinase
Analyse The glycogen-binding domain of the AMP-activated protein kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z0N
- Type
- protein
- Length
- 247 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-AMP-activated protein kinase, beta-1 subunit
- UniProt
- P80386
- Ligands
- GLC
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-AMP-activated protein kinase, beta-1 subunit | protein | 87 | 3% helix, 56% strand | P80386 |
| B, C | 5'-AMP-activated protein kinase, beta-1 subunit | protein | 80 | 0% helix, 59% strand | P80386 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 21 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.46 | 0.76 | 22 | empty |
| 2 | 71 | 0.40 | 0.79 | 16 | empty |
| 3 | 64 | 0.33 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 589 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 331 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 1Z0N · the glycogen-binding domain of the AMP-activated protein kinase · the same entry in another collection · chain B against B, TM-score 1.00
- P80386 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit beta-1… · a predicted model of the same protein · chain C against A, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P80386
- Elsewhere: RCSB PDB 1Z0N · PDBe 1Z0N · UniProt P80386
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